HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).
Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.
Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes

Single Molecule Study of the Intrinsically Disordered FG-Repeat Nucleoporin 153

AbstractNucleoporins (Nups), which are intrinsically disordered, form a selectivity filter inside the nuclear pore complex, taking a central role in the vital nucleocytoplasmic transport mechanism. These Nups display a complex and nonrandom amino-acid architecture of phenylalanine glycine (FG)-repeat clusters and intra-FG linkers. How such heterogeneous sequence composition relates to function and could give rise to a transport mechanism is still unclear. Here we describe a combined chemical biology and single-molecule fluorescence approach to study the large human Nup153 FG-domain. In order to obtain insights into the properties of this domain beyond the average behavior, we probed the end-to-end distance (RE) of several ∼50-residues long FG-repeat clusters in the context of the whole protein domain. Despite the sequence heterogeneity of these FG-clusters, we detected a reoccurring and consistent compaction from a relaxed coil behavior under denaturing conditions (RE/RE,RC = 0.99 ± 0.15 with RE,RC corresponding to ideal relaxed coil behavior) to a collapsed state under native conditions (RE/RE,RC = 0.79 ± 0.09). We then analyzed the properties of this protein on the supramolecular level, and determined that this human FG-domain was in fact able to form a hydrogel with physiological permeability barrier properties

The Spin Glass Transition : Exponents and Dynamics

Numerical simulations on Ising Spin Glasses show that spin glass transitions do not obey the usual universality rules which hold at canonical second order transitions. On the other hand the dynamics at the approach to the transition appear to take up a universal form for all spin glasses. The implications for the fundamental physics of transitions in complex systems are addressed.Comment: 4 pages (Latex) with 3 figures (postscript), accepted for publication in Physica

A Low Cost Spacecraft Architecture for Robotic Lunar Exploration Projects

A program of frequent, capable, but affordable lunar robotic missions prior to return of humans to the moon can contribute to the Vision for Space Exploration (VSE) NASA is tasked to execute. The Lunar Reconnaissance Orbiter (LRO) and its secondary payload are scheduled to orbit the moon, and impact it, respectively, in 2008. It is expected that the sequence of missions occurring for approximately the decade after 2008 will place an increasing emphasis on soft landed payloads. These missions are requited to explore intrinsic characteristics of the moon, such as hydrogen distribution in the regolith, and levitated dust, to demonstrate the ability to access and process in-situ resources, and to demonstrate functions critical to supporting human presence, such as automated precision navigation and landing. Additional factors governing the design of spacecraft to accomplish this diverse set of objectives are: operating within a relatively modest funding profile, the need tb visit multiple sites (both polar and equatorial) repeatedly, and to use the current generation of launch vehicles. In the US, this implies use of the Evolved Expendable Launch Vehicles, or EELVs, although this design philosophy may be extended to launch vehicles of other nations, as well. Many of these factors are seemingly inconsistent with each other. For example, the cost of a spacecraft usually increases with mass; therefore the desire to fly frequent, modestly priced spacecraft seems to imply small spacecraft (< 1 Mt, injected mass). On the other hand, the smallest of the EELVs will inject approx. 3 Mt. on a Trans Lunar Injection (TLI) trajectory md would therefore be wasteful or launching a single, small spacecraft. Increasing the technical capability of a spacecraft (such as autonomous navigation and soft landing) also usually increases cost. A strategy for spacecraft design that meets these conflicting requirements is presented. Taken together, spacecraft structure and propulsion subsystems constitute the majority of spacecraft mass; saving development and integration cost on these elements is critical to controlling cost. Therefore, a low cost, modular design for spacecraft structure and propulsion subsystems is presented which may be easily scaled up or down for either insertion into lunar orbit or braking for landing on the lunar surface. In order to effectively use the approx.3 Mt mass-to-TLI of the EELV, two low cost spacecraft will be manifested on the same launch. One spacecraft will be located on top of the other for launch and the two will have to be released in sequence in order to achieve all mission objectives. The two spacecraft could both be landers, both orbiters, or one lander and one orbiter. In order to achieve mass efficiency, the body of the spacecraft will serve the dual purposes of carrying launch loads and providing attachment points for all the spacecraft subsystems. In order to avoid unaffordable technology development costs, small liquid propulsion components and autonomous, scene-matching navigation cameras may be adapted from military missile programs in order to execute precision soft landings